Replication NAND gate with light as input and output

Samiappan, Manickasundaram; Dadon, Zehavit; Ashkenasy, Gonen

doi:10.1039/c0cc04098c

Cited by 50 publications

(30 citation statements)

References 30 publications

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“…The template dimer then dissociates into two T molecules, readily availablet oc ontinue the catalytic process. In as econd-order catalytic model,w hich is consistent with many recent experiments, [12] at emplate dimer forms aq uaternary intermediate complex with the two fragments,w hich ligate and form at emplate trimer that then dissociates. Schematic diagrams for each of these processes are shown in Figure 1.…”

Section: Introductionsupporting

confidence: 83%

Bistability and Bifurcation in Minimal Self‐Replication and Nonenzymatic Catalytic Networks

et al. 2017

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Bistability and bifurcation, found in a wide range of biochemical networks, are central to the proper function of living systems. We investigate herein recent model systems that show bistable behavior based on nonenzymatic self‐replication reactions. Such models were used before to investigate catalytic growth, chemical logic operations, and additional processes of self‐organization leading to complexification. By solving for their steady‐state solutions by using various analytical and numerical methods, we analyze how and when these systems yield bistability and bifurcation and discover specific cases and conditions producing bistability. We demonstrate that the onset of bistability requires at least second‐order catalysis and results from a mismatch between the various forward and reverse processes. Our findings may have far‐reaching implications in understanding early evolutionary processes of complexification, emergence, and potentially the origin of life.

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Section: Introductionsupporting

confidence: 83%

Bistability and Bifurcation in Minimal Self‐Replication and Nonenzymatic Catalytic Networks

et al. 2017

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“…However, these alternative dynamics can be explicitly controlled by seeding the system in specific ways, rather than relying on spontaneous reactions. By manipulating the peptide networks discussed here (or their close analogs) it has thus been shown, both experimentally and theoretically, that it is possible to perform (simple) computations and network motifs …”

Section: Discussionmentioning

confidence: 99%

The Influence of Modularity, Seeding, and Product Inhibition on Peptide Autocatalytic Network Dynamics

2018

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Chemical networks often exhibit emergent, systems-level properties that cannot be simply derived from the linear sum of the individual components. The design and analysis of increasingly complex chemical networks thus constitute a major area of research in Systems Chemistry. In particular, much research is focused on the emergence of functional properties in prebiotic chemical networks relevant to the origin and early evolution of life. Here, we apply a formal framework known as RAF theory to study the dynamics of a complex network of mutually catalytic peptides. We investigate in detail the influence of network modularity, initial template seeding, and product inhibition on the network dynamics. We show that these results can be useful for designing new experiments, and further argue how they are relevant to origin of life studies.

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“…In order to construct the replication NAND gate [9,75], we have coupled the förster resonance energy transfer (FRET) system with a light-induced replication protocol (Figure 2.7) [76]. This allowed fast in situ tracking of the replication processes (Figure 2.9a), obtaining results that are more accurate than before in terms of reproducibility in repeating experiments, and even yielding some direct insight into the replication mechanism.…”

Section: Light-induced Logic Operationsmentioning

confidence: 99%

Peptide‐Based Computation: Switches, Gates, and Simple Arithmetic

Dadon

Samiappan

Wagner

et al. 2012

Biomolecular Information Processing

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IntroductionBoolean algebra deals with the ''0'' and ''1'' values, utilized as presentations of false and true statements, respectively. The Boolean logic thus provides simple and concise means to describe the output of chemical processes that depend on more than one factor. Historically, the study of chemical logic gates has started with the design of small organic molecules that perform the desired functions when triggered by simple entities such as protons, hydroxyls, or metal ions [1,2]. Since the first demonstration by de Silva, many different chemical logic systems were developed, including metal-organic complexes, peptides, and DNA. The response of these systems to additional chemical triggers, as well as to electrochemical and light triggers, has been demonstrated quite frequently [3][4][5][6][7]. Interestingly, many of the recently described logic operations, and also the more complex arithmetic units, were designed based on pursuing dynamic processes instead of simple binding to one operating molecule [8][9][10][11][12][13][14][15][16][17][18][19][20][21][22][23][24]. Beyond the basic demonstrations, scientists were able to exploit their new gates as smart devices that control various applications such as catalysis, sensing analytes, drug delivery, and even in vivo transcription. In a related line of research, modules of large biochemical systems have also been described to function as Boolean entities, in studies that used the ''top-down'' screening for such operations [25][26][27][28][29][30][31]. This chapter describes primarily our own research, in which we use synthetic networks made of small proteins as tools for performing chemical computations. We do so by practicing both the bottom-up approach, using individual molecules as gates, and the top-down approach, for which the entire molecular network is used to perform the desired functionality.Biology can serve as inspiration and can provide chemists with the design principles for engineering networks of interacting and replicating molecules. These can potentially be used as controllable tools for studying systems behavior. Toward this aim, different research groups have designed and characterized dynamic combinatorial libraries [32][33][34][35][36][37][38] and replication networks made of nucleic acids (DNA and RNA) [39][40][41][42], peptides [43][44][45][46], and small organic molecules [47][48][49][50].

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Replication NAND gate with light as input and output

Cited by 50 publications

References 30 publications

Bistability and Bifurcation in Minimal Self‐Replication and Nonenzymatic Catalytic Networks

Bistability and Bifurcation in Minimal Self‐Replication and Nonenzymatic Catalytic Networks

The Influence of Modularity, Seeding, and Product Inhibition on Peptide Autocatalytic Network Dynamics

Peptide‐Based Computation: Switches, Gates, and Simple Arithmetic

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